ArtiaX/pandas/numpy problem in 1.4

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Linux-5.3.18-150300.59.71-default-x86_64-with-glibc2.31
ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.4 (2022-06-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> toolshed show

Downloading bundle ChimeraX_ArtiaX-0.3-py3-none-any.whl  

Errors may have occurred when running pip:  

pip standard error:  
\---  
WARNING: Value for scheme.platlib does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /fs/home/kaufman/.local/share/ChimeraX/1.4/site-packages  
sysconfig: /fs/home/kaufman/.local/lib/python3.9/site-packages  
WARNING: Value for scheme.purelib does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /fs/home/kaufman/.local/share/ChimeraX/1.4/site-packages  
sysconfig: /fs/home/kaufman/.local/lib/python3.9/site-packages  
WARNING: Value for scheme.headers does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /fs/home/kaufman/.local/share/ChimeraX/include/python3.9/ChimeraX-
ArtiaX  
sysconfig: /fs/home/kaufman/.local/include/python3.9/ChimeraX-ArtiaX  
WARNING: Value for scheme.scripts does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /fs/home/kaufman/.local/share/ChimeraX/bin  
sysconfig: /fs/home/kaufman/.local/bin  
WARNING: Value for scheme.data does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /fs/home/kaufman/.local/share/ChimeraX  
sysconfig: /fs/home/kaufman/.local  
WARNING: Additional context:  
user = True  
home = None  
root = None  
prefix = None  
WARNING: Value for scheme.headers does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /fs/home/kaufman/.local/share/ChimeraX/include/python3.9/UNKNOWN  
sysconfig: /fs/home/kaufman/.local/include/python3.9/UNKNOWN  
WARNING: You are using pip version 21.3.1; however, version 24.0 is available.  
You should consider upgrading via the '/fs/pool/pool-
bmapps/hpcl5S15/app/soft/CHIMERAX/1.4/bin/ChimeraX -m pip install --upgrade
pip' command.  
\---  

pip standard output:  
\---  
Looking in indexes: https://pypi.org/simple,
https://cxtoolshed.rbvi.ucsf.edu/pypi/  
Processing /fs/home/kaufman/Downloads/ChimeraX_ArtiaX-0.3-py3-none-any.whl  
Installing collected packages: ChimeraX-ArtiaX  
Attempting uninstall: ChimeraX-ArtiaX  
Found existing installation: ChimeraX-ArtiaX 0.3  
Uninstalling ChimeraX-ArtiaX-0.3:  
Successfully uninstalled ChimeraX-ArtiaX-0.3  
Successfully installed ChimeraX-ArtiaX-0.3  
\---  

Successfully installed ChimeraX-ArtiaX-0.3  
Installed ChimeraX-ArtiaX (0.3)  
Replacing data format 'Artiatomi Motivelist' as defined by ChimeraX-ArtiaX
with definition from ChimeraX-ArtiaX  
Replacing data format 'Generic Particle List' as defined by ChimeraX-ArtiaX
with definition from ChimeraX-ArtiaX  
Replacing data format 'Dynamo Table' as defined by ChimeraX-ArtiaX with
definition from ChimeraX-ArtiaX  
Replacing data format 'RELION STAR file' as defined by ChimeraX-ArtiaX with
definition from ChimeraX-ArtiaX  
Replacing data format 'Coords file' as defined by ChimeraX-ArtiaX with
definition from ChimeraX-ArtiaX  
Replacing data format 'PEET mod/csv' as defined by ChimeraX-ArtiaX with
definition from ChimeraX-ArtiaX  
Replacing data format 'ArtiaX geometric model' as defined by ChimeraX-ArtiaX
with definition from ChimeraX-ArtiaX  

Overriding existing toolbar provider for toolbar provider 'Launch' in bundle
'ChimeraX-ArtiaX'  

Overriding existing toolbar provider for toolbar provider 'Help' in bundle
'ChimeraX-ArtiaX'  

Overriding existing toolbar provider for toolbar provider 'XY' in bundle
'ChimeraX-ArtiaX'  

Overriding existing toolbar provider for toolbar provider 'XZ' in bundle
'ChimeraX-ArtiaX'  

Overriding existing toolbar provider for toolbar provider 'YZ' in bundle
'ChimeraX-ArtiaX'  

Overriding existing toolbar provider for toolbar provider 'Invert Selection'
in bundle 'ChimeraX-ArtiaX'  

Overriding existing toolbar provider for toolbar provider 'Sphere' in bundle
'ChimeraX-ArtiaX'  

Overriding existing toolbar provider for toolbar provider 'Line' in bundle
'ChimeraX-ArtiaX'  

Overriding existing toolbar provider for toolbar provider 'Surface' in bundle
'ChimeraX-ArtiaX'  

Overriding existing toolbar provider for toolbar provider 'Boundary' in bundle
'ChimeraX-ArtiaX'  

Overriding existing toolbar provider for toolbar provider 'Triangles From
Links' in bundle 'ChimeraX-ArtiaX'  

Overriding existing toolbar provider for toolbar provider 'Triangulate' in
bundle 'ChimeraX-ArtiaX'  

Overriding existing toolbar provider for toolbar provider 'Remove Selected' in
bundle 'ChimeraX-ArtiaX'  

Overriding existing toolbar provider for toolbar provider 'Create Mask' in
bundle 'ChimeraX-ArtiaX'  

> ui tool show ArtiaX

Traceback (most recent call last):  
File "/fs/home/kaufman/.local/share/ChimeraX/1.4/site-
packages/pandas/__init__.py", line 26, in <module>  
from pandas.compat import (  
File "/fs/home/kaufman/.local/share/ChimeraX/1.4/site-
packages/pandas/compat/__init__.py", line 26, in <module>  
from pandas.compat.numpy import is_numpy_dev  
File "/fs/home/kaufman/.local/share/ChimeraX/1.4/site-
packages/pandas/compat/numpy/__init__.py", line 21, in <module>  
raise ImportError(  
ImportError: this version of pandas is incompatible with numpy < 1.22.4  
your numpy version is 1.22.1.  
Please upgrade numpy to >= 1.22.4 to use this pandas version  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "/fs/pool/pool-bmapps/hpcl5S15/app/soft/CHIMERAX/1.4/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 559, in start_tool  
ti = api._api_caller.start_tool(api, session, self, tool_info)  
File "/fs/pool/pool-bmapps/hpcl5S15/app/soft/CHIMERAX/1.4/lib/python3.9/site-
packages/chimerax/core/toolshed/__init__.py", line 1325, in start_tool  
return cls._get_func(api, "start_tool")(session, bi, ti)  
File "/fs/home/kaufman/.local/share/ChimeraX/1.4/site-
packages/chimerax/artiax/__init__.py", line 27, in start_tool  
from . import tool  
File "/fs/home/kaufman/.local/share/ChimeraX/1.4/site-
packages/chimerax/artiax/tool.py", line 28, in <module>  
from .ArtiaX import (  
File "/fs/home/kaufman/.local/share/ChimeraX/1.4/site-
packages/chimerax/artiax/ArtiaX.py", line 13, in <module>  
from .io import open_particle_list, save_particle_list, get_fmt_aliases  
File "/fs/home/kaufman/.local/share/ChimeraX/1.4/site-
packages/chimerax/artiax/io/__init__.py", line 8, in <module>  
from .RELION import RELION_FORMAT  
File "/fs/home/kaufman/.local/share/ChimeraX/1.4/site-
packages/chimerax/artiax/io/RELION/__init__.py", line 3, in <module>  
from .RELIONParticleData import RELION_FORMAT  
File "/fs/home/kaufman/.local/share/ChimeraX/1.4/site-
packages/chimerax/artiax/io/RELION/RELIONParticleData.py", line 5, in <module>  
import starfile  
File "/fs/home/kaufman/.local/share/ChimeraX/1.4/site-
packages/starfile/__init__.py", line 1, in <module>  
from .functions import read, write  
File "/fs/home/kaufman/.local/share/ChimeraX/1.4/site-
packages/starfile/functions.py", line 9, in <module>  
from .parser import StarParser  
File "/fs/home/kaufman/.local/share/ChimeraX/1.4/site-
packages/starfile/parser.py", line 9, in <module>  
import pandas as pd  
File "/fs/home/kaufman/.local/share/ChimeraX/1.4/site-
packages/pandas/__init__.py", line 31, in <module>  
raise ImportError(  
ImportError: C extension: None not built. If you want to import pandas from
the source directory, you may need to run 'python setup.py build_ext' to build
the C extensions first.  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/fs/pool/pool-bmapps/hpcl5S15/app/soft/CHIMERAX/1.4/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 1685, in <lambda>  
run(ses, "ui tool show %s" % StringArg.unparse(tool_name)))  
File "/fs/pool/pool-bmapps/hpcl5S15/app/soft/CHIMERAX/1.4/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "/fs/pool/pool-bmapps/hpcl5S15/app/soft/CHIMERAX/1.4/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "/fs/pool/pool-bmapps/hpcl5S15/app/soft/CHIMERAX/1.4/lib/python3.9/site-
packages/chimerax/ui/cmd.py", line 219, in ui_tool_show  
bi.start_tool(session, name)  
File "/fs/pool/pool-bmapps/hpcl5S15/app/soft/CHIMERAX/1.4/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 564, in start_tool  
raise ToolshedError(  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool ArtiaX in
bundle ChimeraX-ArtiaX:  
C extension: None not built. If you want to import pandas from the source
directory, you may need to run 'python setup.py build_ext' to build the C
extensions first.  
  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool ArtiaX in
bundle ChimeraX-ArtiaX:  
C extension: None not built. If you want to import pandas from the source
directory, you may need to run 'python setup.py build_ext' to build the C
extensions first.  
  
File "/fs/pool/pool-bmapps/hpcl5S15/app/soft/CHIMERAX/1.4/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 564, in start_tool  
raise ToolshedError(  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 470.103.01
OpenGL renderer: Tesla K80/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.9.11
Locale: en_US.UTF-8
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: xcb

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=xfce
XDG_SESSION_DESKTOP=
XDG_CURRENT_DESKTOP=XFCE
DISPLAY=:5.0
DCV_GL_DISPLAY=:0.1
Manufacturer: FUJITSU
Model: PRIMERGY CX2570 M1
OS: SLES 15.3 
Architecture: 64bit ELF
Virtual Machine: none
CPU: 36 Intel(R) Xeon(R) CPU E5-2699 v3 @ 2.30GHz
Cache Size: 46080 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:          503Gi       203Gi       288Gi       4.2Gi        12Gi       293Gi
	Swap:          31Gi          0B        31Gi

Graphics:
	07:00.0 VGA compatible controller [0300]: Matrox Electronics Systems Ltd. MGA G200e [Pilot] ServerEngines (SEP1) [102b:0522]	
	Subsystem: Fujitsu Technology Solutions Device [1734:11cc]	
	Kernel driver in use: mgag200

Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.10.1
    backcall: 0.2.0
    blockdiag: 3.0.0
    certifi: 2022.5.18.1
    cftime: 1.6.0
    charset-normalizer: 2.0.12
    ChimeraX-AddCharge: 1.2.3
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.4.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-ArtiaX: 0.3
    ChimeraX-Atomic: 1.39.1
    ChimeraX-AtomicLibrary: 7.0
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.1
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.7
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.1
    ChimeraX-CommandLine: 1.2.3
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.4
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1.1
    ChimeraX-LinuxSupport: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.6
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.7
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.5.5
    ChimeraX-ModelPanel: 1.3.2
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.9
    ChimeraX-PDB: 2.6.6
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.6
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.8
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.0.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.1
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.18.3
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.26
    debugpy: 1.6.0
    decorator: 5.1.1
    distro: 1.6.0
    docutils: 0.17.1
    entrypoints: 0.4
    filelock: 3.4.2
    fonttools: 4.33.3
    funcparserlib: 1.0.0
    geomdl: 5.3.1
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.27
    imagecodecs: 2021.11.20
    imagesize: 1.3.0
    ipykernel: 6.6.1
    ipython: 7.31.1
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.0.3
    jupyter-client: 7.1.0
    jupyter-core: 4.10.0
    kiwisolver: 1.4.2
    line-profiler: 3.4.0
    lxml: 4.7.1
    lz4: 3.1.10
    MarkupSafe: 2.1.1
    matplotlib: 3.5.1
    matplotlib-inline: 0.1.3
    msgpack: 1.0.3
    nest-asyncio: 1.5.5
    netCDF4: 1.5.8
    networkx: 2.6.3
    numexpr: 2.8.1
    numpy: 1.26.4
    openvr: 1.16.802
    packaging: 21.3
    pandas: 2.2.0
    ParmEd: 3.4.3
    parso: 0.8.3
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.0.1
    pip: 21.3.1
    pkginfo: 1.8.2
    prompt-toolkit: 3.0.29
    psutil: 5.9.0
    ptyprocess: 0.7.0
    pycollada: 0.7.2
    pydicom: 2.2.2
    Pygments: 2.11.2
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.0
    PyQt6-Qt6: 6.3.0
    PyQt6-sip: 13.3.1
    PyQt6-WebEngine-commercial: 6.3.0
    PyQt6-WebEngine-Qt6: 6.3.0
    python-dateutil: 2.8.2
    pytz: 2022.1
    pyzmq: 23.1.0
    qtconsole: 5.3.0
    QtPy: 2.1.0
    RandomWords: 0.3.0
    requests: 2.27.1
    scipy: 1.7.3
    setuptools: 59.8.0
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.3.2
    sphinx-autodoc-typehints: 1.15.2
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    starfile: 0.5.4
    suds-community: 1.0.0
    superqt: 0.6.1
    tables: 3.7.0
    tifffile: 2021.11.2
    tinyarray: 1.2.4
    tornado: 6.1
    traitlets: 5.1.1
    typing-extensions: 4.9.0
    tzdata: 2024.1
    urllib3: 1.26.9
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.1
    wheel-filename: 1.3.0

[pett]

Apparently ArtiaX pandas/numpy dependencies don't work in ChimeraX 1.4. Not sure if this is a toolshed installation problem, or just that ArtiaX 0.3 should not be declared as working with ChimeraX 1.3+ on the toolshed.

[Greg Couch]

Confirmed that it works in ChimeraX 1.5.dev202210202150, 1.7, and 1.9.dev202405202323. Will change the toolshed entry for ArtiaX 0.3 to require ChimeraX 1.5.